1
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Wang Y, Shi N, He Y, Li Y, Zheng Q. A direct approach toward investigating DNA-ligand interactions via surface-enhanced Raman spectroscopy combined with molecular dynamics simulations. Phys Chem Chem Phys 2023; 25:2153-2160. [PMID: 36562542 DOI: 10.1039/d2cp04566d] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Small molecules that interfere with DNA replication can trigger genomic instability, which makes these molecules valuable in the search for anticancer drugs. Thus, interactions between DNA and its ligands at the molecular level are of great significance. In the present study, a new method based on surface-enhanced Raman spectroscopy (SERS) combined with molecular dynamics simulations has been proposed for analyzing the interactions between DNA and its ligands. The SERS signals of DNA hairpins (ST: d(CGACCAACGTGTCGCCTGGTCG), AP1: d(CGCACAACGTGTCGCCTGTGCG)), pure argininamide, and their complexes, were obtained, and the characteristic peak sites of the DNA secondary structure and argininamide ligand-binding region were analyzed. Molecular dynamics calculations predicted that argininamide binds to the 8C and 9G bases of AP1 via hydrogen bonding. Our method successfully detected the changes of SERS fingerprint peaks of hydrogen bonds and bases between argininamide and DNA hairpin bases, and their binding sites and action modes were consistent with the predicted results of the molecular dynamics simulations. This SERS technology combined with the molecular dynamics simulation detection platform provides a general analysis tool, with the advantage of effective, rapid, and sensitive detection. This platform can obtain sufficient molecular level conformational information to provide avenues for rapid drug screening and promote progress in several fields, including targeted drug design.
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Affiliation(s)
- Yunpeng Wang
- College of Pharmacy, Research Center for Innovative Technology of Pharmaceutical Analysis, Harbin Medical University, Harbin, Heilongjiang, 150081, China.
| | - Na Shi
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130023, China.
| | - Yingying He
- College of Pharmacy, Research Center for Innovative Technology of Pharmaceutical Analysis, Harbin Medical University, Harbin, Heilongjiang, 150081, China.
| | - Yang Li
- College of Pharmacy, Research Center for Innovative Technology of Pharmaceutical Analysis, Harbin Medical University, Harbin, Heilongjiang, 150081, China.
| | - Qingchuan Zheng
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130023, China.
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2
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Chauhan N, Karanastasis A, Ullal CK, Wang X. Homologous pairing in short double-stranded DNA-grafted colloidal microspheres. Biophys J 2022; 121:4819-4829. [PMID: 36196058 PMCID: PMC9811663 DOI: 10.1016/j.bpj.2022.09.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/04/2022] [Accepted: 09/28/2022] [Indexed: 01/07/2023] Open
Abstract
Homologous pairing (HP), i.e., the pairing of similar or identical double-stranded DNA, is an insufficiently understood fundamental biological process. HP is now understood to also occur without protein mediation, but crucial mechanistic details remain poorly established. Unfortunately, systematic studies of sequence dependence are not practical due to the enormous number of nucleotide permutations and multiple possible conformations involved in existing biophysical strategies even when using as few as 150 basepairs. Here, we show that HP can occur in DNA as short as 18 basepairs in a colloidal microparticle-based system. Exemplary systematic studies include resolving opposing reports of the impact of % AT composition, validating the impact of nucleotide order and triplet framework and revealing isotropic bendability to be crucial for HP. These studies are enabled by statistical analysis of crystal size and fraction within coexisting fluid-crystal phases of double-stranded DNA-grafted colloidal microspheres, where crystallization is predicated by HP.
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Affiliation(s)
- Neha Chauhan
- Department of Materials Science and Engineering, Rensselaer Polytechnic Institute, Troy, New York
| | - Apostolos Karanastasis
- Department of Materials Science and Engineering, Rensselaer Polytechnic Institute, Troy, New York
| | - Chaitanya K Ullal
- Department of Materials Science and Engineering, Rensselaer Polytechnic Institute, Troy, New York
| | - Xing Wang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois; Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois.
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3
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Bespalova M, Behjatian A, Karedla N, Walker-Gibbons R, Krishnan M. Opto-Electrostatic Determination of Nucleic Acid Double-Helix Dimensions and the Structure of the Molecule–Solvent Interface. Macromolecules 2022; 55:6200-6210. [PMID: 35910310 PMCID: PMC9330769 DOI: 10.1021/acs.macromol.2c00657] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
A DNA molecule is
highly electrically charged in solution. The
electrical potential at the molecular surface is known to vary strongly
with the local geometry of the double helix and plays a pivotal role
in DNA–protein interactions. Further out from the molecular
surface, the electrical field propagating into the surrounding electrolyte
bears fingerprints of the three-dimensional arrangement of the charged
atoms in the molecule. However, precise extraction of the structural
information encoded in the electrostatic “far field”
has remained experimentally challenging. Here, we report an optical
microscopy-based approach that detects the field distribution surrounding
a charged molecule in solution, revealing geometric features such
as the radius and the average rise per basepair of the double helix
with up to sub-Angstrom precision, comparable with traditional molecular
structure determination techniques like X-ray crystallography and
nuclear magnetic resonance. Moreover, measurement of the helical radius
furnishes an unprecedented view of both hydration and the arrangement
of cations at the molecule–solvent interface. We demonstrate
that a probe in the electrostatic far field delivers structural and
chemical information on macromolecules, opening up a new dimension
in the study of charged molecules and interfaces in solution.
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Affiliation(s)
- Maria Bespalova
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Ali Behjatian
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Narain Karedla
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Rowan Walker-Gibbons
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Madhavi Krishnan
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
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4
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Behjatian A, Krishnan M. Electrostatic free energies carry structural information on nucleic acid molecules in solution. J Chem Phys 2022; 156:134201. [DOI: 10.1063/5.0080008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Over the last several decades, a range of experimental techniques from x-ray crystallography and atomic force microscopy to nuclear magnetic resonance and small angle x-ray scattering have probed nucleic acid structure and conformation with high resolution both in the condensed state and in solution. We present a computational study that examines the prospect of using electrostatic free energy measurements to detect 3D conformational properties of nucleic acid molecules in solution. As an example, we consider the conformational difference between A- and B-form double helices whose structures differ in the values of two key parameters—the helical radius and rise per basepair. Mapping the double helix onto a smooth charged cylinder reveals that electrostatic free energies for molecular helices can, indeed, be described by two parameters: the axial charge spacing and the radius of a corresponding equivalent cylinder. We show that electrostatic free energies are also sensitive to the local structure of the molecular interface with the surrounding electrolyte. A free energy measurement accuracy of 1%, achievable using the escape time electrometry (ET e) technique, could be expected to offer a measurement precision on the radius of the double helix of approximately 1 Å. Electrostatic free energy measurements may, therefore, not only provide information on the structure and conformation of biomolecules but could also shed light on the interfacial hydration layer and the size and arrangement of counterions at the molecular interface in solution.
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Affiliation(s)
- Ali Behjatian
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Madhavi Krishnan
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
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5
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Saran R, Wang Y, Li ITS. Mechanical Flexibility of DNA: A Quintessential Tool for DNA Nanotechnology. SENSORS (BASEL, SWITZERLAND) 2020; 20:E7019. [PMID: 33302459 PMCID: PMC7764255 DOI: 10.3390/s20247019] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/04/2020] [Accepted: 12/04/2020] [Indexed: 02/06/2023]
Abstract
The mechanical properties of DNA have enabled it to be a structural and sensory element in many nanotechnology applications. While specific base-pairing interactions and secondary structure formation have been the most widely utilized mechanism in designing DNA nanodevices and biosensors, the intrinsic mechanical rigidity and flexibility are often overlooked. In this article, we will discuss the biochemical and biophysical origin of double-stranded DNA rigidity and how environmental and intrinsic factors such as salt, temperature, sequence, and small molecules influence it. We will then take a critical look at three areas of applications of DNA bending rigidity. First, we will discuss how DNA's bending rigidity has been utilized to create molecular springs that regulate the activities of biomolecules and cellular processes. Second, we will discuss how the nanomechanical response induced by DNA rigidity has been used to create conformational changes as sensors for molecular force, pH, metal ions, small molecules, and protein interactions. Lastly, we will discuss how DNA's rigidity enabled its application in creating DNA-based nanostructures from DNA origami to nanomachines.
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Affiliation(s)
- Runjhun Saran
- Department of Chemistry, Biochemistry and Molecular Biology, Irving K. Barber Faculty of Science, The University of British Columbia, Kelowna, BC V1V1V7, Canada;
| | - Yong Wang
- Department of Physics, Materials Science and Engineering Program, Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Isaac T. S. Li
- Department of Chemistry, Biochemistry and Molecular Biology, Irving K. Barber Faculty of Science, The University of British Columbia, Kelowna, BC V1V1V7, Canada;
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6
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O' Lee DJ. Introducing a model of pairing based on base pair specific interactions between identical DNA sequences. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:075102. [PMID: 29219116 DOI: 10.1088/1361-648x/aaa043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
At present, there have been suggested two types of physical mechanism that may facilitate preferential pairing between DNA molecules, with identical or similar base pair texts, without separation of base pairs. One mechanism solely relies on base pair specific patterns of helix distortion being the same on the two molecules, discussed extensively in the past. The other mechanism proposes that there are preferential interactions between base pairs of the same composition. We introduce a model, built on this second mechanism, where both thermal stretching and twisting fluctuations are included, as well as the base pair specific helix distortions. Firstly, we consider an approximation for weak pairing interactions, or short molecules. This yields a dependence of the energy on the square root of the molecular length, which could explain recent experimental data. However, analysis suggests that this approximation is no longer valid at large DNA lengths. In a second approximation, for long molecules, we define two adaptation lengths for twisting and stretching, over which the pairing interaction can limit the accumulation of helix disorder. When the pairing interaction is sufficiently strong, both adaptation lengths are finite; however, as we reduce pairing strength, the stretching adaptation length remains finite but the torsional one becomes infinite. This second state persists to arbitrarily weak values of the pairing strength; suggesting that, if the molecules are long enough, the pairing energy scales as length. To probe differences between the two pairing mechanisms, we also construct a model of similar form. However, now, pairing between identical sequences solely relies on the intrinsic helix distortion patterns. Between the two models, we see interesting qualitative differences. We discuss our findings, and suggest new work to distinguish between the two mechanisms.
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Affiliation(s)
- Dominic J O' Lee
- Department of Chemistry, Imperial College London, SW7 2AZ, London, United Kingdom
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7
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Cortini R, Cheng X, Smith JC. The tilt-dependent potential of mean force of a pair of DNA oligomers from all-atom molecular dynamics simulations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:084002. [PMID: 28092632 DOI: 10.1088/1361-648x/aa4e68] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Electrostatic interactions between DNA molecules have been extensively studied experimentally and theoretically, but several aspects (e.g. its role in determining the pitch of the cholesteric DNA phase) still remain unclear. Here, we performed large-scale all-atom molecular dynamics simulations in explicit water and 150 mM sodium chloride, to reconstruct the potential of mean force (PMF) of two DNA oligomers 24 base pairs long as a function of their interaxial angle and intermolecular distance. We find that the potential of mean force is dominated by total DNA charge, and not by the helical geometry of its charged groups. The theory of homogeneously charged cylinders fits well all our simulation data, and the fit yields the optimal value of the total compensated charge on DNA to ≈65% of its total fixed charge (arising from the phosphorous atoms), close to the value expected from Manning's theory of ion condensation. The PMF calculated from our simulations does not show a significant dependence on the handedness of the angle between the two DNA molecules, or its size is on the order of [Formula: see text]. Thermal noise for molecules of the studied length seems to mask the effect of detailed helical charge patterns of DNA. The fact that in monovalent salt the effective interaction between two DNA molecules is independent on the handedness of the tilt may suggest that alternative mechanisms are required to understand the cholesteric phase of DNA.
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Affiliation(s)
- Ruggero Cortini
- Chemistry Department, Faculty of Natural Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK. Laboratoire de Physique Théorique de la Matière Condensée, CNRS UMR 7600, Université Pierre et Marie Curie, Sorbonne Université, 4 place Jussieu, 75252 Cedex 05, Paris, France. Genome Architecture, Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain. Universitat Pompeu Fabra (UPF), Barcelona, Spain
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8
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O' Lee DJ, Danilowicz C, Rochester C, Kornyshev AA, Prentiss M. Evidence of protein-free homology recognition in magnetic bead force-extension experiments. Proc Math Phys Eng Sci 2016; 472:20160186. [PMID: 27493568 PMCID: PMC4971244 DOI: 10.1098/rspa.2016.0186] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Earlier theoretical studies have proposed that the homology-dependent pairing of large tracts of dsDNA may be due to physical interactions between homologous regions. Such interactions could contribute to the sequence-dependent pairing of chromosome regions that may occur in the presence or the absence of double-strand breaks. Several experiments have indicated the recognition of homologous sequences in pure electrolytic solutions without proteins. Here, we report single-molecule force experiments with a designed 60 kb long dsDNA construct; one end attached to a solid surface and the other end to a magnetic bead. The 60 kb constructs contain two 10 kb long homologous tracts oriented head to head, so that their sequences match if the two tracts fold on each other. The distance between the bead and the surface is measured as a function of the force applied to the bead. At low forces, the construct molecules extend substantially less than normal, control dsDNA, indicating the existence of preferential interaction between the homologous regions. The force increase causes no abrupt but continuous unfolding of the paired homologous regions. Simple semi-phenomenological models of the unfolding mechanics are proposed, and their predictions are compared with the data.
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Affiliation(s)
- D J O' Lee
- Department of Chemistry , Imperial College London , London SW7 2AZ, UK
| | - C Danilowicz
- Department of Physics , Harvard University, Cambridge , MA 02138, USA
| | - C Rochester
- Department of Chemistry , Imperial College London , London SW7 2AZ, UK
| | - A A Kornyshev
- Department of Chemistry , Imperial College London , London SW7 2AZ, UK
| | - M Prentiss
- Department of Physics , Harvard University, Cambridge , MA 02138, USA
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9
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O' Lee DJ, Wynveen A, Albrecht T, Kornyshev AA. Which way up? Recognition of homologous DNA segments in parallel and antiparallel alignments. J Chem Phys 2015; 142:045101. [PMID: 25638008 DOI: 10.1063/1.4905291] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Homologous gene shuffling between DNA molecules promotes genetic diversity and is an important pathway for DNA repair. For this to occur, homologous genes need to find and recognize each other. However, despite its central role in homologous recombination, the mechanism of homology recognition has remained an unsolved puzzle of molecular biology. While specific proteins are known to play a role at later stages of recombination, an initial coarse grained recognition step has, however, been proposed. This relies on the sequence dependence of the DNA structural parameters, such as twist and rise, mediated by intermolecular interactions, in particular, electrostatic ones. In this proposed mechanism, sequences that have the same base pair text, or are homologous, have lower interaction energy than those sequences with uncorrelated base pair texts. The difference between the two energies is termed the "recognition energy." Here, we probe how the recognition energy changes when one DNA fragment slides past another, and consider, for the first time, homologous sequences in antiparallel alignment. This dependence on sliding is termed the "recognition well." We find there is a recognition well for anti-parallel, homologous DNA tracts, but only a very shallow one, so that their interaction will differ little from the interaction between two nonhomologous tracts. This fact may be utilized in single molecule experiments specially targeted to test the theory. As well as this, we test previous theoretical approximations in calculating the recognition well for parallel molecules against MC simulations and consider more rigorously the optimization of the orientations of the fragments about their long axes upon calculating these recognition energies. The more rigorous treatment affects the recognition energy a little, when the molecules are considered rigid. When torsional flexibility of the DNA molecules is introduced, we find excellent agreement between the analytical approximation and simulations.
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Affiliation(s)
- Dominic J O' Lee
- Department of Chemistry, Imperial College London, SW7 2AZ London, United Kingdom
| | - Aaron Wynveen
- School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Tim Albrecht
- Department of Chemistry, Imperial College London, SW7 2AZ London, United Kingdom
| | - Alexei A Kornyshev
- Department of Chemistry, Imperial College London, SW7 2AZ London, United Kingdom
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10
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Sebastiani F, Pietrini A, Longo M, Comez L, Petrillo C, Sacchetti F, Paciaroni A. Melting of DNA Nonoriented Fibers: A Wide-Angle X-ray Diffraction Study. J Phys Chem B 2014; 118:3785-92. [DOI: 10.1021/jp411096d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Federico Sebastiani
- Dipartimento
di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
- CNR,
Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento
di Fisica, Università degli Studi di Perugia, I-06123 Perugia, Italy
| | - Alberto Pietrini
- Dipartimento
di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
| | - Marialucia Longo
- Dipartimento
di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
- Elettra − Sincrotrone Trieste, I-34149 Basovizza, Trieste, Italy
| | - Lucia Comez
- Dipartimento
di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
- CNR,
Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento
di Fisica, Università degli Studi di Perugia, I-06123 Perugia, Italy
| | - Caterina Petrillo
- Dipartimento
di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
| | - Francesco Sacchetti
- Dipartimento
di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
- CNR,
Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento
di Fisica, Università degli Studi di Perugia, I-06123 Perugia, Italy
| | - Alessandro Paciaroni
- Dipartimento
di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
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11
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Lee D. Effect of undulations on spontaneous braid formation. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:022719. [PMID: 24032876 DOI: 10.1103/physreve.88.022719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Indexed: 06/02/2023]
Abstract
This paper is an extension of a recent study where it was shown that forces dependent on molecular helical structure may cause two DNA molecules to spontaneously braid [R. Cortini et al., Biophys. J. 101, 875 (2011)]. Here, bending fluctuations of molecular center lines about the braid axis are incorporated into the braiding theory, which may be generalized to other helix-dependent interactions and other helical molecules. The free energy of the pair of molecules is recalculated and compared to its value without incorporating undulations. We find that the loss of configurational entropy due to confinement of the molecules in the braid is quite high. This contribution to the free energy increases the amount of attraction needed for spontaneous braiding due to helix-dependent forces. The theory will be further developed for plectonemes and braids under mechanical forces in later work.
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Affiliation(s)
- Dominic Lee
- Department of Chemistry, Imperial College London, London SW7 2AZ, United Kingdom
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